Abstract:
:The apicomplexan Cryptosporidium parvum is one of the most prevalent protozoan parasites of humans. We report the physical mapping of the genome of the Iowa isolate, sequencing and analysis of chromosome 6, and approximately 0.9 Mbp of sequence sampled from the remainder of the genome. To construct a robust physical map, we devised a novel and general strategy, enabling accurate placement of clones regardless of clone artefacts. Analysis reveals a compact genome, unusually rich in membrane proteins. As in Plasmodium falciparum, the mean size of the predicted proteins is larger than that in other sequenced eukaryotes. We find several predicted proteins of interest as potential therapeutic targets, including one exhibiting similarity to the chloroquine resistance protein of Plasmodium. Coding sequence analysis argues against the conventional phylogenetic position of Cryptosporidium and supports an earlier suggestion that this genus arose from an early branching within the Apicomplexa. In agreement with this, we find no significant synteny and surprisingly little protein similarity with Plasmodium. Finally, we find two unusual and abundant repeats throughout the genome. Among sequenced genomes, one motif is abundant only in C. parvum, whereas the other is shared with (but has previously gone unnoticed in) all known genomes of the Coccidia and Haemosporida. These motifs appear to be unique in their structure, distribution and sequences.
journal_name
Genome Resjournal_title
Genome researchauthors
Bankier AT,Spriggs HF,Fartmann B,Konfortov BA,Madera M,Vogel C,Teichmann SA,Ivens A,Dear PHdoi
10.1101/gr.1555203subject
Has Abstractpub_date
2003-08-01 00:00:00pages
1787-99issue
8eissn
1088-9051issn
1549-5469pii
1555203journal_volume
13pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::A DNA mutation detection protocol able to identify and characterize a previously unknown change in a given sequence in a rapid, efficient, sensitive, and inexpensive manner is required to take advantage of the resources now available to researchers through the genome sequencing projects. We have developed a method bas...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.gr-1578r
更新日期:2002-09-01 00:00:00
abstract::Detecting rare sequence variants in genomic DNA is central to the analysis of de novo mutation and recombination events and the detection of rare pathological mutations in mixed cell populations. Current PCR techniques suffer from noise that limits detection to variants present at a frequency of at least 10(-4)-10(-5)...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1214603
更新日期:2003-10-01 00:00:00
abstract::Understanding the consequences of regulatory variation in the human genome remains a major challenge, with important implications for understanding gene regulation and interpreting the many disease-risk variants that fall outside of protein-coding regions. Here, we provide a direct window into the regulatory consequen...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.155192.113
更新日期:2014-01-01 00:00:00
abstract::We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales linearly with the number of samples, enabling analysis of whole-genome data in large cohorts. Our approach is based on ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.081398.108
更新日期:2009-02-01 00:00:00
abstract::Double minutes (dmin) and homogeneously staining regions (hsr) are the cytogenetic hallmarks of genomic amplification in cancer. Different mechanisms have been proposed to explain their genesis. Recently, our group showed that the MYC-containing dmin in leukemia cases arise by excision and amplification (episome model...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.106252.110
更新日期:2010-09-01 00:00:00
abstract::A-to-I RNA editing is a conserved widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions, mainly noncoding. Mutations in ADAR enzymes in Caenorhabditis elegans cause defects in normal development but are not lethal as in human and mouse. ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.211169.116
更新日期:2017-03-01 00:00:00
abstract::RNA interference is a powerful tool for studying gene function and for drug target discovery in diverse organisms and cell types. In mammalian systems, small interfering RNAs (siRNAs), or DNA plasmids expressing these siRNAs, have been used to down-modulate gene expression. However, inefficient transfection protocols,...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1332603
更新日期:2003-10-01 00:00:00
abstract::Genomics data introduce a substantial computational burden as well as data privacy and ownership issues. Data sets generated by high-throughput sequencing platforms require immense amounts of computational resources to align to reference genomes and to call and annotate genomic variants. This problem is even more pron...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.207464.116
更新日期:2018-09-01 00:00:00
abstract::RNA-seq by poly(A) selection is currently the most common protocol for whole transcriptome sequencing as it provides a broad, detailed, and accurate view of the RNA landscape. Unfortunately, the utility of poly(A) libraries is greatly limited when the input RNA is degraded, which is the norm for research tissues and c...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.189621.115
更新日期:2015-09-01 00:00:00
abstract::Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-base...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.235820.118
更新日期:2018-12-01 00:00:00
abstract::DNA is a universal language encrypted with biological instruction for life. In higher organisms, the genetic information is preserved predominantly in an organized exon/intron structure. When a gene is expressed, the exons are spliced together to form the transcript for protein synthesis. We have developed a complexit...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.313703
更新日期:2003-02-01 00:00:00
abstract::A small set of core transcription factors (TFs) dominates control of the gene expression program in embryonic stem cells and other well-studied cellular models. These core TFs collectively regulate their own gene expression, thus forming an interconnected auto-regulatory loop that can be considered the core transcript...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.197590.115
更新日期:2016-03-01 00:00:00
abstract::CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome Sequencing Project (RGSP), a hybrid strategy of "clone by clone" and "whole genome shotgun" approaches was used to maximize the...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2171704
更新日期:2004-04-01 00:00:00
abstract::Chromosome-specific cDNA libraries are new tools for the isolation of genes from specific genomic regions. We have used two YACs than span the approximately 2-Mb cri-du-chat critical region (CDCCR) of chromosome 5p to directly screen a chromosome 5-specific (CH5SP) fetal brain cDNA library. To compare this library wit...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7.2.118
更新日期:1997-02-01 00:00:00
abstract::By applying graph representations to biochemical pathways, a new computational pipeline is proposed to find potential operons in microbial genomes. The algorithm relies on the fact that enzyme genes in operons tend to catalyze successive reactions in metabolic pathways. We applied this algorithm to 42 microbial genome...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.200602
更新日期:2002-08-01 00:00:00
abstract::It is widely accepted that newly arisen duplicate gene pairs experience an altered selective regime that is often manifested as an increase in the rate of protein sequence evolution. Many details about the nature of the rate acceleration remain unknown, however, including its typical magnitude and duration, and whethe...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6341207
更新日期:2008-01-01 00:00:00
abstract::Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these hu...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.219493.116
更新日期:2017-09-01 00:00:00
abstract::Nucleosomes containing the CenH3 (CENPA or CENP-A) histone variant replace H3 nucleosomes at centromeres to provide a foundation for kinetochore assembly. CENPA nucleosomes are part of the constitutive centromere associated network (CCAN) that forms the inner kinetochore on which outer kinetochore proteins assemble. T...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.204784.116
更新日期:2016-09-01 00:00:00
abstract::Paternal X chromosome inactivation occurs in rodent extraembryonic membranes and in all tissues of marsupials. Methylation of CpG islands occurs on the inactive X in eutherians and is considered to be a stabilizing mechanism. The only previous study of a marsupial X-linked CpG island was of the G6PD gene of the Virgin...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.2.114
更新日期:1996-02-01 00:00:00
abstract::We have constructed a detailed map of the genomic region containing the ETS-variant gene 6 (ETV6), involved in translocations and deletions associated with hematologic malignancies. Thirty-eight cosmids were characterized belonging to two contigs spanning 340 kb, and an EcoRl restriction map was developed. The gap bet...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.5.404
更新日期:1996-05-01 00:00:00
abstract::The dense RFLP linkage map of tomato (Lycopersicon esculentum) contains >300 anonymous cDNA clones. Of those clones, 272 were partially or completely sequenced. The sequences were compared at the DNA and protein level to known genes in databases. For 57% of the clones, a significant match to previously described genes...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.8.842
更新日期:1998-08-01 00:00:00
abstract::Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process are subject to strong selective constraint. While some studies show that highly constrained noncoding regions act to enhance transcription...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.083089.108
更新日期:2008-12-01 00:00:00
abstract::Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the dominant technique for mapping transcription factor (TF) binding regions genome-wide. We performed an integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium. We ident...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.139105.112
更新日期:2012-09-01 00:00:00
abstract::In diploid mammalian genomes, parental alleles can exhibit different methylation patterns (allele-specific DNA methylation, ASM), which have been documented in a small number of cases except for the imprinted regions and X chromosomes in females. We carried out a chromosome-wide survey of ASM across 16 human pluripote...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.104695.109
更新日期:2010-07-01 00:00:00
abstract::In contrast to other animal cell lines, the chicken pre-B cell lymphoma line, DT40, exhibits a high level of homologous recombination, which can be exploited to generate site-specific alterations in defined target genes or regions. In addition, the ability to generate human/chicken monochromosomal hybrids in the DT40 ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.6.666
更新日期:1998-06-01 00:00:00
abstract::Translocations are a common class of chromosomal aberrations and can cause disease by physically disrupting genes or altering their regulatory environment. Some translocations, apparently balanced at the microscopic level, include deletions, duplications, insertions, or inversions at the molecular level. Traditionally...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.122986.111
更新日期:2011-10-01 00:00:00
abstract::One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identification in terms of ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.122800
更新日期:2000-10-01 00:00:00
abstract::Aberrations of protein-coding genes are a focus of cancer genomics; however, the impact of oncogenes on expression of the ~50% of transcripts without protein-coding potential, including long noncoding RNAs (lncRNAs), has been largely uncharacterized. Activating mutations in the BRAF oncogene are present in >70% of mel...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.140061.112
更新日期:2012-06-01 00:00:00
abstract::Obesity is reaching epidemic proportions in developed countries and represents a significant risk factor for hypertension, heart disease, diabetes, and dyslipidemia. Splicing mutations constitute at least 14% of disease-causing mutations, thus implicating polymorphisms that affect splicing as likely candidates for dis...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6661308
更新日期:2008-02-01 00:00:00
abstract::CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.136101.111
更新日期:2012-09-01 00:00:00